Interaction types criteria

All interactions in ContactMaps have been calculated using GetContacts. In this page we explain the criteria used in GetContacts to calculate non-covalent interactions. Images by Rasmus Fonseca and Anthony Ma (https://getcontacts.github.io/interactions.html).

Van der waals
|AB| < Rvdw(A) + Rvdw(B) + 0.5

A and B are any non-hydrogen atoms

Ligands supported

Hydrophobic
|AB| < Rvdw(A) + Rvdw(B) + 0.5

A, B: ALA+CYS+PHE+GLY+ILE+LEU+MET+PRO+VAL+TRP and element C or S

Ligands supported

Hydrogen bond
|AD| < 3.5Å
∠AHD < 70°

Where A (acceptor) and D (donor) are any atom except hydrogen, carbon or sulphur.

Ligands supported

Water bridge

Consists of two different residues forming an Hydrogen bond with the same water molecule

Ligands supported

Extended Water bridge

Consists of two different residues forming an Hydrogen bond with two different water moleucules which also form an hydrogen bond between them

Ligands supported

Salt bridge
|AC| < 4.0Å

A (anion): ASP/OD1+OD2, GLU/OE1+OE2
C (cation): LYS/NZ, ARG/NH1+NH2, HIS/ND1+NE2

Ligands not supported

Pi-cation
|AC| < 6.0Å
∠CAn < 60°

A (aromatic): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2), center(HIS/CG+CD2+CE1)
C (cation): LYS/NZ, ARG/NH1+NH2, HIS/ND1+NE2

Ligands not supported

Pi-stacking
|A1A2| < 7.0Å
∠(n1, n2) < 30°
∠(n1, A1A2) < 45°
∠(n2, A1A2) < 45°

A1, A2 (aromatic rings): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2), center(HIS/CG+CD2+CE1)

Ligands not supported

T-stacking
|A1A2| < 5.0Å
60° < ∠(n1, n2) < 90°
∠(n1, A1A2) < 45°
∠(n2, A1A2) < 45°

A1, A2 (aromatic rings): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2), center(HIS/CG+CD2+CE1)

Ligands not supported